# GSE156455
###### tags: 研究

## Resourses

paper: https://pubmed.ncbi.nlm.nih.gov/33125872/
dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156455

## Prerequisite

### macOS
#### 1. Install VSCode via Homebrew
- Open Terminal app
- Run `/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"`
- Run `brew install git`
- Run `brew install --cask visual-studio-code`

#### 2. Install Python via [asdf](https://asdf-vm.com/)
- Open VSCode app
- Invoke command palette: `Cmd+Shift+P`
- Type `terminal` and select `Terminal: Create New Terminal`
- Run `git clone https://github.com/asdf-vm/asdf.git ~/.asdf --branch v0.10.2`
- Run below in once

tee -a ~/.zshrc << EOF
. $HOME/.asdf/asdf.sh
# append completions to fpath
fpath=(${ASDF_DIR}/completions $fpath)
# initialise completions with ZSH's compinit
autoload -Uz compinit && compinit
EOF
exec $SHELL -l

- Run `asdf plugin-add python`
- Run `asdf install python 3.10.8 && asdf global python 3.10.8`
#### 3. Install Python extension for VSCode
- Select the Extensionstab on the left sidebar
- Search for Python
- Install Python extension


### Windows
#### 1. Install WSL2
- Open PowerShell in administrator mode
- Run `wsl --install` or `wsl --install -d Ubuntu`

ref: https://learn.microsoft.com/en-us/windows/wsl/install

#### 2. Install VSCode
from: https://code.visualstudio.com/download

#### 3. Install WSL extension
- Select the Extensionstab on the left sidebar
- Search for WSL
- Install WSL extension


#### 4. Change default terminal
- Restart VSCode
- Invoke command palette: `Ctrl+Shift+P`
- Type `default` ans select "Terminal: Select Default Profile"
- Select "Ubuntu(WSL)"

#### 5. Install Python via [asdf](https://asdf-vm.com/)
- Type `terminal` and select `Terminal: Create New Terminal`
- Run `sudo apt install curl git build-essential libssl-dev zlib1g-dev
libbz2-dev libreadline-dev libsqlite3-dev wget llvm
libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev`
- Run `git clone https://github.com/asdf-vm/asdf.git ~/.asdf --branch v0.10.2`
- Run below in once

tee -a ~/.bashrc << EOF
. $HOME/.asdf/asdf.sh
. $HOME/.asdf/completions/asdf.bash
EOF
exec $SHELL -l

- Run `asdf plugin-add python`
- Run `asdf install python 3.10.8 && asdf global python 3.10.8`

#### 6. Install Python extension for VSCode
- Select the Extensionstab on the left sidebar
- Search for Python
- Install Python extension


## Dataset
> Single-cell transcriptional atlas of the developing Drosophila visual system. A transcriptional atlas covers 9 stages of pupal development (every 12 hours).
:::info
### .tsv
Tab Separated Values (.tsv) format, like the Conma Separeted Values (.csv) format, is often used to represent tabular data.
### .mtx
It is a format for efficiently representing sparse matrices and is not a human readable format, so a detailed description is omitted.
:::
:::success
`early`: 0,12,24h
`main`: 24,36,48,60,72,84,96h
:::
- GSE156455_barcodes_(early|main).tsv
- List of cell identifiers
- Columns
- `barcode`: cell ids, e.g. 'DGRP_All_A_2_TGATTTCGTCATCCGG'
- GSE156455_features_(early|main).tsv
- List of cell features
- Colmuns
- `feature_id`: transcript ids, e.g. 'FBgn0038498'
- `feature_name`: gene names, e.g. 'beat-IIa'
- `feature_type`: feature types, e.g. 'Gene Expression'
- GSE156455_metadata_(early|main).tsv
- List of metadata for each cell
- Colmuns
- barcode: cellID
- set: W1118 or DGRP datasets
- rep: biological replicate (A/B)
- trep: technical replicate (i.e. a single 10X library, see sampleID format below)
- genotype: W1118 or DGRP strain (based on demultiplexing)
- time: timepoint
- class: cell class
- type: cell type or cluster identity
- subtype: cell subtype (if not applicable, same as type)
- GSE156455_matrix_(early|main).mtx
- Sparse matrix of gene expression levels per cell
- Row: feature
- Colmun: cell
- GSE156455_tsne_(early|main).tsv
- t-SNE results
- see: https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding

## Programing Basics

TODO

## Analysis
- Run `git clone https://github.com/FujishigeTemma/GSE156455.git /path/to/anywhere/you/want` (replace destination path)
- if you don't know `path` or `directory` see: https://desktop.arcgis.com/en/arcmap/10.6/tools/supplement/pathnames-explained-absolute-relative-unc-and-url.htm
- Open downloaded folder with VSCode
- Open Terminal
- Run `pip install -r requirements.txt`
- Work with `coexpression.ipynb`